bkgdCorrect {codelink} | R Documentation |
Takes a Codelink object with Spot mean and Bkgd median values and corrects applying one of the methods available.
bkgdCorrect(object, method="half", preserve=FALSE, verbose=TRUE, offset=0)
object |
character; an object of class "Codelink". |
method |
character; the correction method to use, one of "none", "subtract", "half" and "normexp". |
preserve |
logical; if Smean and Bmedian slots should be preserved. |
verbose |
logical; if TRUE print some information with method normexp. |
offset |
numeric; value to add to intensities. |
Available methods are: . None: Left intensities untouched. . Subtract: Simple subtraction of Bkgd median from Spot mean. . Half: The same as above but aboid negative values setting all intensity values below zero to 0.5. . Normexp: Apply normexp background adjustment from package limma.
An object of class Codelink with corrected intensity values, that is Ri slot.
Diego Diez
# data(codelink.example) # codelink.example <- bkgdCorrect(codelink.example, method="half")